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How to optimize stack height of .wig files in IGB

Hi,

I am trying to compare several .wig files of RNA sequencing data in IGB. The choose stack height and optimise stack height tabs are unavailable when I have a. wig file track highlighted but they are available when I have the annotation .gff file track highlighted. For my analysis I want to be able to scan the genome by eye and then use the optimise stack height option.

Thanks,
Sarah

igb
• 3,438 views • link
updated by Ram Ram • written by s.murdoch • s.murdoch

1 answer

Hi Sarah,

The .wig files are considered graphs in IGB. The equivalent to optimizing stack height for a graph file would be to adjust the Y-axis of the graph so that it is displaying all of the data.

  1. Highlight the .wig file track
  2. Click on the Graph tab
  3. Drag the rightmost slider under the Y Axis Scale all the way to the right

You can also highlight all of your .wig files, and then adjust the Y Axis Scale under the Graph tab. This will put all of the files on the same scale, allowing you to quickly compare between samples.

You can take this one step further and put all of the .wig files into the same track for easy comparison.

  1. Highlight all of the .wig file tracks
  2. Click on Join within the Operations box in the Graph tab
  3. Highlight the Joined Graphs track that was produced
  4. Collapse the track to overlay all of the graphs

Hope this helps!

Nowlan

• 1 views • link
updated by Ram Ram • written by Nowlan Freese Nowlan Freese

Hi,

Thanks so much for your advice, it has been very helpful!

Sarah :)

• 0 views • link
written by s.murdoch • s.murdoch

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